Although both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) techniques have been interfaced with high resolution tandem mass spectrometers (MS) only MALDI tandem MS (or MS/MS) is currently suitable for high throughput applications in proteomics and glycomics. The ESI-MS/MS throughput is usually limited by slow liquid chromatography (LC) technique usually utilized in conjunction with ESI-MS/MS instrumentation. The purpose of this proposal is to develop a new high resolution and high throughput ESI tandem mass spectrometer for important applications in proteomics and glycomics, including increasing throughput of protein identification and structure elucidation, characterization of post-translational modifications, and relative quantitation to distinguish differential expression of proteins. The new instrument design is based on efficient and fully independent multi-channel high resolution tandem MS in which vacuum system, data and control system, and substantial part of electronics and mass analyzer are shared between all MS channels, resulting in substantial cost reduction and increase of throughput of the total MS system by interfacing one MS to multiple LC systems. The application of proteomics and glycomics tools plays an important role in modern life sciences, drug discovery, and clinical applications. We propose a new technology for increasing throughput of protein identification and structure elucidation using mass spectrometry, an essential strategy in proteomics and glycomics today. [unreadable] [unreadable] [unreadable]